


Trials and tribulations

by Anonymous



Category: HLVRAI - Fandom
Genre: Backstory, Unethical Science, bubby prototypes, coomer clones, critique welcome, gotta up those writer strats, please i've written like only one reserach paper before, research articles, tommy fucked up and evil science moments
Language: English
Status: Completed
Published: 2021-02-23
Updated: 2021-02-23
Packaged: 2021-03-13 12:21:23
Rating: Mature
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 3
Words: 3,615
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/29651250
Author URL: https://archiveofourown.org/
Summary: The trials for an immortal dog. It's not wholesome.
Comments: 4
Kudos: 5
Collections: Anonymous





	1. Chapter 1

**Author's Note:**

> Alt story for this was gonna be wholesome and Tommy basically creating Sunkist and being like "oh my small dog friend, i see no flaws (despite her being a 2D png), perfect in my eyes" and he does a buncha research and acts like a new parent and experiences the trials and joys of having a puppy. But like, what he did unethical science?
> 
> There's two endings so choose which one you want.

The metal office door clicked behind Gordon like a crisp leaf crunching in fall. The dim, plain walls were enhanced by the colorful, predominantly yellow toys and assorted writing utensils lined up along the table. This was Tommy’s office. 

Gordon had been having trouble with his research paper recently and Tommy offered to show Gordon a couple of his he’d written over the years. Actually, “a couple” was a major understatement. Tommy had written almost a hundred research papers to the present date. The boxes of old papers on the bookshelf were optimistically organized into different subjects, ranging from biology (Tommy’s major) to physics. The physics box was definitely lighter than the majority of the other boxes and had a thick coat of dust on it, signifying that it hadn’t been touched in a while. Until now! 

He pulled the box out, pausing as there was the sound of crinkling paper. Gordon looked to the box in confusion, trying to figure out what was causing that sound. He tried moving the box and once again heard the paper crinkling sound. He sighed and figured that the paper was going to crumple regardless of what he did so he opted to pull out the box fully. 

Gordon pulled the crushed research paper out from its hiding spot in the back of the shelf and shook it to get the dust off. The paper was carelessly wedged between the box and the shelf, forgotten. The paper seemed relatively old, and was most likely an old paper for a class Tommy couldn’t bring himself to throw out. Gordon had a couple of lackluster essays he felt sentimental himself so he understood why some of the paper would be this old. He straightened out the paper and curiously checked for the date of the paper before noticing that it was actually Tommy’s doctorate. The paper was pretty old, the date being the same year Gordon got his high school diploma. 

He had never read Tommy’s doctorate nor had Tommy really talked about the paper’s title. It must have been an underhand published paper as that happens to some of the college students collaborating with Black Mesa on their doctorate. It wasn’t really uncommon at Black Mesa because they simply wanted their soon-to-be employees to graduate as fast as possible even at the expense of proper procedure. That isn’t to say that the graduates didn’t have the proper knowledge to have the title. Sometimes, the ethical approval supervisors were paid off for a quicker process.

Gordon, out of curiosity, flipped the page and started reading.

_ Introduction _

_ Environmental adaptation is a necessary part of survival. This concept is seen throughout Darwin’s theories on evolution. Based on the changing environment, genes which were more effective were favored. In a sense, the most effective genes for a certain situation would be considered “perfect”. However, these changes to become effective in an environment occurred slowly over several generations. With the variety of situations and environment specimens are placed in, it’s practically impossible to adapt and become perfect suited for each environment through traditional means such as natural evolution. This is where human intervention comes into play. Throughout history, humans have undergone selective breeding for plants and animals which artificially choose more effective, or more “perfect” genes for their needs. In the 1900s, instead of these genes changing naturally due to genetic malformations, radiation was used to speed up these defects in order to produce a variety of different traits humans would then selectively breed. This paper aims to figure out a way to produce an effective and stable way in order to produce a “perfect” specimen which adapts its DNA rapidly to its environment when necessary. The methods section will evaluate a variety of different techniques which may contribute to rapid adaptations to certain environments such as radiation, CRISPR gene editing and protein folding. The paper will conclude with a discussion on the most effective results as well as methods to improve said results to become more stable and faster…. _

Radiation? As a kid, Gordon had thought about superpowers, specifically the ones relating to shapeshifting. He pondered on this, noting that radiation was an odd choice. Genetic mutations induced by radiation were uncontrollable and damaging. Even if you were to control the mutations through methods such as protein folding, the process would be slow. If the process was sped up, the rapid rewriting of all the DNA in all the cells would most likely be extremely painful.

_ Literature Review  _

_ Gene Expression Changes  _

_ DNA has the capability to change its genetic expression based on the situation. During NASA’s Twin Study, it was discovered that DNA expression can change when exposed to intense environments such as outer space (NASA). Environmental changes do cause DNA expression to occur naturally, however, it does not change the DNA itself. Black Mesa’s Bubby Advanced Alteration Prototype Project (BAAPP) has a history experimenting with these dynamic changes of DNA expression and led Bubby subjects to have morphing abilities which allowed them to adapt to extreme environments within one to two business days(Keller & Cross, 1967). The BAAPP subjects were altered to have all known genetic traits embedded in the DNA, a hyperactive mRNA production and produce excess phosphorylation which produces more polypeptide chains and causes more reactions to occur thus making changes in DNA expression faster. The reason all genetic traits were embedded in the DNA was so that traits could be moved to being expressed based on the environment. In addition to that, the enzymes of BAAPP subjects were changed to respond more radically to environmental stresses which led to varying different protein folds which leads to a profound effect on cellular structure and function. This DNA expression was even mildly examined when the air condition temperatures remained colder than usual, resulting in the majority of the BAAPP subjects spontaneously growing hair(Keller & Cross, 1968). Further BAAPP subjects were able to trigger their forms into shifting into various household objects, such as cars or potted plants. However, the rapid change in DNA expression often put strain on the cells because the concept relies on protein folding, leading to most BAAPP subjects bodies degrading quickers than usual and within months of conception, develop a case of The Crumbles, an incurable disease which leads the body to crumble apart into dust.  _

_ Participants in the Subject Integration Morph Project (SIMP) fared slightly better, with having an increase in shapeshifting ability due to having a database of various DNA from different mammals to choose which enzymes to activate or not, however, the inability to control enzymes lead to the majority of these participants to develop defects such as multiple uncontrollable limbs, rapid-onset Alzheimer (due to a drastic increase in N-APP enzymes) as well as immortality(Green & Coolatta, 1984).  _

_ Gene Expression Stabilities _

_ In addition to rapid changes in gene expression due to changes in environment, gene expression can also be kept the same despite extreme changes in environment. In the Biotoxic Uniform Stability and Sustainability Yields (BUSSY), volunteers from the Coomer Clones (CC) were modified in order to prevent the denaturing of proteins and DNA within extreme environments. By replacing the hydrogen bonds which occur naturally in proteins with much stronger covalent bonds, proteins remained the same despite exposure to potentially denaturing situations such as heat, acidity and varying salt concentrations(Egon, 1956). However, in doing this, all proteins remain rigid and lead to no changes in muscle growth or loss. In addition to this, the CC also contained cells which rarely divided, leading to immunity against radiation poisoning but also led to inability to heal from minor wounds without medical intervention…. _

Gordon looked at the paper with a sickening feeling beginning to form in the pit of his stomach. The Bubby experiments were already an ethically touchy subject Black Mesa almost got shut down. Black Mesa had never been too good in the ethical sector from its beginning. Though, to find out this information, Gordon had to imagine the amount of clones and prototypes that the facility had to go through. It was similar to the mile-long lists for infomercials medicines which listed symptoms such as nausea, urge to drink orange juice and, most notably, death. To write those warnings on the product, some poor person had to experience those events during a test trial or something. But, he wasn’t going to apply the immoral things Black Mesa did to Tommy and his research. Though, a little voice started chewing in the back of his brain, suggesting that Tommy might have gone through Black Mesa because his paper was barred for being “too unethical”.

_ Methods _

_ This section outlines the progress and experiments done to the lab-grown pure golden retriever test subjects. The reason golden retrievers were chosen was due to their comprehensive intelligence, cooperative nature and response to commands. The dogs were divided up into three groups, each group consisting of 100 dog embryos with rapidly dividing cells. The first group has targeted releases of radiation as well as rapidly dividing cells which denatures DNA and proteins allowing the subject to quickly shapeshift between certain states with the cells constantly being rewritten. The second group will have the DNA edited directly via CRISPR to prevent any evidence of the Crumbles occuring while the subject is still in control of the aspects with newly introduced xenian blood. The third group will have the Coomer Clone covalent bond protein stabilities along with the Bubby Protype hyperactive enzymes… _

Gordon paused to think again as more and more questions were running through his head the further he read. How many dogs did he go through until he got Sunkist, the perfect dog? Were the other dogs still alive? Were there dogs too powerful and immoral to ever be killed? 

_...the defects some of the subjects experienced consisted of unwanted immortality, inability to choose a stable form and turning to goop, teleportation between dimensions along with nearby objects, radioactivity and internal/external bleeding. These were disposed of appropriately, the salvageable ones donated to local hospitals as service dogs and the unsalvageable, immoral ones locked away...  _

There was a large empty building nearby the Black Mesa facility, but Gordon didn’t realize it was a hospital until now. The dogs outlined in the experiment didn’t seem necessarily perfectly safe and sound. Some of the side effects involved radioactive waste and teleportation afterall. But, the fact that some of the immoral dogs were locked away made Gordon uneasy. Dogs with the inability to be anything else but goop due to rapid transformation and radiation were most likely in a lot of pain and their immortality allowed for no end to it. The subjects were most likely still locked away, forgotten, waiting in their sad, boring, painful existence because they weren’t perfect and Tommy threw them away without trying to fix them, continuing to strive for perfection. 

Gordon didn’t want to read further, the sterile language of the research paper denoting the loss of life as nothing, nothing but a complication in the pursuit of knowledge. Besides, he didn’t need to finish the paper as he already knew the result--Sunkist, the eerily tame and responsible husk of a dog. Gordon felt sick to his stomach and stepped outside to take a breather. It was too bright in the office, the joyful colors once comforting and welcoming now smiling in a more sinister yet mocking way. He left the paper discarded on the ground, right next to the box he pulled it from. 

One of the sentences in the conclusion caught his eye. It was after the limitations section, the “future studies” section. It implied that this method could be applied to humans so that they could be as powerful and as perfect as ever. But, that was impossible. Humans can’t be perfect as it’s in their nature to change and improve, only remaining stagnant in death. To make humans perfect would cause them to cease being human. Gordon was snapped out of his thoughts by a small tap on his head. He looked up to see Benrey of all people, holding a small pipe he ripped out of someplace somewhere, like a kid picking up a random stick. 

“Bro, what are you doing out here? Do yo- do you have a license? Your passport? Why are you in Tommy’s office huh? Stealing...stealing ruth goldbird cubes?” Benrey said, tapping Gordon’s head with the pipe with every question. 

“Benrey- Stop that dude! I was looking through-” Gordon started, swatting away the pipe before pausing and realizing that this was  _ Benrey _ he was talking to. Benrey was a long time friend of Tommy’s so he had to know at least something about the experiments. “Benrey, do you...know?”

“Huh?” Benrey said, snapping back into the conversation. “I know about Tommy. We’re the bestiest bros, bestie friends for life.” 

“I mean the experiments he did! The one with- with  _ Sunkist _ ,” Gordon said, leaning in and lowering his voice cautiously.

“Hey bro, that’s Tommy's favorite soda.”

“Yeah- yeah, you’re right but it’s also the name of his dog?? You know, Sunkist?” 

“Uh, yeah. I helped Tommy with all of his experiments. It was epic he was a- I was a greater helper than any other scientist.”

“Isn’t it wrong?”

“Wrong? Bro, we’re the ones following the Black Mesa regulations but i don’t- i don’t know if you’re following the correct science scientific method,” Benrey said, somewhat accusatory. Gordon frowned slightly, not quite understanding what Benrey meant. Black Mesa barely had any regulations. Did he think that these experiments were...normal? That all scientific experiments went on like this? 

“The Bubby clone experiments, the Coomer experiments, all the other fucked up Black Mesa experiments you knew about??” 

“I don’t understand why you’re- hey it’s not nice to swear, gordon mean-man. Bro, just let the scientist do their science stuff bud. And Tommy’s the best scientist ever. He can follow the science instructions to make a cake perfectly fine.”

Benrey was going to make his headache worse. Gordon waved him off and went back inside to the room, the new information making him feel even worse. Benrey didn’t know any better and thought this experimentation was ethical. He probably didn’t even know what ethics were, judging by his behavior. But, really that was more of a side issue. The real issue was Tommy. How could his friend be the one doing this? How had this horrible evil remained under such a bright and cheery facade? 

The door clicked quietly behind him and Gordon scrambled, his heart pounding as a quick jolt of white-hot fear flashed through his body. 

“How’s it going, Mr. Freeman?” Tommy asked, looking to Gordon with a slight confused expression. Gordon couldn’t even look him in the eye much less look at him the same. Every action Tommy did, his little quirks, his smile, all of that was so carefree from the experiments he conducted. Everything he did, while being fully aware of this, was without guilt or even a sliver of regret. 

Gordon wished Tommy threw the paper away, so that Gordon could live unaware of this. But at the same time, Gordon was glad he found out. He trusted him so much and to still provide that trust while not knowing that Tommy did something like this was terrifying. But although Tommy tried to hide the paper away behind the box, he couldn’t really bring himself to throw it away and forever get rid of it since it was such a large part of his life. It was where he got his pHD from. 

He hoped Tommy had changed. Gordon would ask but, honestly, Gordon is afraid that Tommy hasn’t. Tommy reaches out to touch Gordon’s shoulder to pet him. Gordon always thought it was a little strange that Tommy pet things to comfort them but in the context of this experiment it made sense. It’s because he did this to calm down all the dogs in the past.

“Mr. Freeman? A-are you alright? You look really pale! Like printer paper!” Tommy said, concern lacing his voice. Gordon looked away as far as he could without turning his head, gulping in nervousness. In his head he was begging for this to be a misunderstanding but the amount of evidence and just the situation of the company they worked in assured that any excuse would be impossible. 

“Tommy,” Gordon started, his throat tight almost like he was having an allergic reaction. “Has it ever occurred to you that humans- humans can’t be perfect?”

What? That’s what Tommy said, without even having to make a sound. Gordon felt him draw back in confusion, in bafflement. Maybe the paper was fake afterall. It was getting hard to breathe as all the air in the room was being sucked out towards Tommy. The moment of silence was terrible, like the image of a cup being knocked over or the three little dots appearing when someone is still typing. You know what’s coming and it can not be stopped, but do you really know what it is? 

“What’s that y-you have there?” Tommy said in a light voice, a slight grin on his face as he caught sight of the box of research papers on the ground, the crumpled paper shoddily shoved behind it. With that, Gordon explodes much like a bubble on packaging material: sharp, quick and slicing. 

“You experimented on- on everyone!” 

“So? I also experimented on myself.”

“You- you fused Bubby and Sunkist together. And- and you killed multiple Coomer clones! You know that he feels everything they feel!”

“Not Bubby. B-Bubby prototypes. N-not Coomer. Coomer clones. I still don’t see w-what’s wrong. They’re wasted resources and- and Black Mesa is happy for me to get them off their hands. They- they weren’t perfect so I decided to- to make them perfect.”

Tommy was still the same. It wasn’t a prior mistake or anything but rather a prior achievement. He was proud of his dog, proud of himself, despite those horrendous deeds. It was tempting to disown Tommy right there and then, cut off all communication. But, this was Tommy. Tommy was kind, understanding, witty, affectionate, and most of all, his friend. 

Was there some obscure, absurd thing he was missing? 


	2. Forgiveness

**Summary for the Chapter:**

> Maybe...Tommy isn't that bad?

**Notes for the Chapter:**

> how do i justify animal testing

Gordon wanted to know why. And so, Gordon asked. Tommy explained the research, stating that though it was ethically and morally grey, none of the subjects in his experiments suffered. The Bubby clones were genetically modified so there wasn’t any pain, fear or emotion because that part of the brain just didn’t form. Contained and tubed, nothing really mattered as they were born into a vegetable state. They didn’t have a personal, individual effect on the world and the world didn’t have an effect on them.

Gordon still felt uncomfortable. But, it’s Tommy. Tommy was other things outside of his work, like a hardcore fan of Hello Kitty: Seasons on the Wii and a fan of Beyblades. He liked taking his dog on a walk and going about his schedule as usual. The experiments he did weren't a whole aspect of his personality. And though the dogs remained forever immortal, they weren’t really existing. Sure, they were existing in the sense of in a space but they weren’t really living and the only emotional harm those dogs inflicted were on those observing them. 

Gordon calmed down slightly, still on edge. Tommy moved to pet Gordon’s shoulder again, causing Gordon to realize that, hey, Tommy actually tried his hardest to minimize the pain and suffering of his subjects. The pets were most likely just to at least provide some normality within the experiments just on the off chance the dogs could feel something positive. Tommy was a good guy. 

And with that, Gordon and Tommy moved on, burying this event under more fond memories.


	3. Disowning

**Summary for the Chapter:**

> I can't believe it. Tommy did some really unethical science. Nothing can go back to normal.

"Tommy do- does your dad even know about all of the fucked up shit you did?!"

"Not at all Mr. Freeman. And- and I doubt- even if he did, he'd still love me,” Tommy said, crossing his arms somewhat defensively. 

This was wrong. The animal testing. The experiments. Tommy didn’t even treat the Bubby clones like humans. He probably didn’t even inform Coomer, causing the man to experience long term phantom pains. The immortal dogs were waiting and rotting away for some impossible day. Even after all these years of having a phd, Tommy’s mind remained the same. This wasn’t okay. It was utterly disgusting. 

And it wasn’t like Gordon could separate Tommy from this experiment. It was the reason which caused him to get a phd! It’d be better if Tommy grew from this mistake and regretted it but how could he ever if he didn’t see it as a mistake? Judging by how crumpled up the paper was and how little he talked about it, Tommy seemed to know it was wrong to a degree. But even by trying to minimize the pain in the research, it wasn’t justifiable. It was still unethical. 

“I want nothing to do with you. Please,” Gordon said, looking down at the ground. He glanced at Tommy’s shoes, sharpie doodles of stars and dogs on the canvas. It didn’t matter who or what else Tommy was. This thinking was all wrong. If his views on life and his ideals on everything lead to something like this being acceptable enough to action upon, what else would he have exceptions for? Ideals are applied on all actions. 

“Gordon, it’s- it’s still me,” Tommy said, attempting to plead with him. Gordon walked out of the office and out of Tommy’s life. The door shut behind him in a defining click, sealing the deal.

It wasn’t him anymore.

**Author's Note:**

> Also like, the reason it's two business days specifically is because we weren't there on the weekends so we can't tell if the morphing abilities work then. It's unscientific to assume so without measuring and none of them wanted to work on the weekend.


End file.
